Alignments for a candidate for fadA in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Desulfacinum infernum DSM 9756

Align FadA (EC 2.3.1.16) (characterized)
to candidate WP_073041505.1 BUB04_RS16425 acetyl-CoA C-acyltransferase

Query= metacyc::G1G01-2278-MONOMER
         (391 letters)



>NCBI__GCF_900129305.1:WP_073041505.1
          Length = 398

 Score =  287 bits (734), Expect = 4e-82
 Identities = 163/394 (41%), Positives = 242/394 (61%), Gaps = 7/394 (1%)

Query: 3   LNPRDVVIVDFGRTPMGRS-KGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWGC 61
           + PRDVV+VD  RT  G++ + G+   TRA+DM   +I +L+ RN +V P+ VE+ +WG 
Sbjct: 1   MKPRDVVLVDGIRTAFGKAGEKGIFWMTRADDMVVKVIRELMRRNPQVKPEMVEENVWGA 60

Query: 62  VNQTLEQGWNIARMASLMTPIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGG 121
             Q  +QG  + R  +++  +  ++A  +V R+C   M+A+  AA  I  G  D+ + GG
Sbjct: 61  TTQEGDQGLTMGRTTAILAGLSESTAGYSVDRMCAGGMTAVTCAASEIAMGACDIAIAGG 120

Query: 122 VEHMGHVSMMHGVDPNPHLSLH--AAKASGMMGLTAEMLGKMHG-ITREQQDLFGLRSHQ 178
           VEHMGH  M    DPNP        ++ + +MG TAE L  M   IT+E  D + L   +
Sbjct: 121 VEHMGHHPMGATADPNPRFLTEKLVSEDALVMGKTAENLHDMFPEITKEMADEYALLCQK 180

Query: 179 LAHKATVEGKFKDEIIPMQGYDENGFLKVFDFDETIRPETTLEGLASLKPAFNPKGGTVT 238
            A KA  EGK +  I+PM  Y +NG++ V D DE  RP+TTLEGLASL+  F  +G  VT
Sbjct: 181 KAFKAYQEGKIQKMIVPMTVYTKNGWV-VADRDEQPRPDTTLEGLASLRTPFRVQG-KVT 238

Query: 239 AGTSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVPSTQKALKR 298
            G +S + DGA  +++M+ ++A +LG++P   +   A AGV P IMGYGP+PST+K L R
Sbjct: 239 PGNASGLNDGACGVLLMTAEKAKELGLKPKMRLVGYAFAGVKPEIMGYGPIPSTKKVLAR 298

Query: 299 AGLTMADIDFIELNEAFAAQALPVLKDLKVLDKMDEKVNLHGGAIALGHPFGCSGARISG 358
            GL   D+D +ELNEAFA QA+  +++  +    D+++N +GGAIA GHP   SG R+  
Sbjct: 299 TGLKFDDLDVVELNEAFAVQAIAFMREFGMKFPDDKRLNPYGGAIAFGHPLASSGPRLMV 358

Query: 359 TLLNVMKQN-GGTLGVATMCVGLGQGITTVFERV 391
            L++  +++     G+ATMCVGLGQG + ++E +
Sbjct: 359 HLMHYFEEHPEARYGLATMCVGLGQGGSVIWENL 392


Lambda     K      H
   0.319    0.134    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 437
Number of extensions: 23
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 391
Length of database: 398
Length adjustment: 31
Effective length of query: 360
Effective length of database: 367
Effective search space:   132120
Effective search space used:   132120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_073041505.1 BUB04_RS16425 (acetyl-CoA C-acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01930.hmm
# target sequence database:        /tmp/gapView.20784.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-129  417.6   0.0   2.6e-129  417.4   0.0    1.0  1  lcl|NCBI__GCF_900129305.1:WP_073041505.1  BUB04_RS16425 acetyl-CoA C-acylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073041505.1  BUB04_RS16425 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.4   0.0  2.6e-129  2.6e-129       2     385 .]       9     390 ..       8     390 .. 0.95

  Alignments for each domain:
  == domain 1  score: 417.4 bits;  conditional E-value: 2.6e-129
                                 TIGR01930   2 vdavRtpig..klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 
                                               vd++Rt++g    +g +  ++a+d++++vi+el++r+ +++pe ++e ++G+++q+g+q  +++R+ a+
  lcl|NCBI__GCF_900129305.1:WP_073041505.1   9 VDGIRTAFGkaGEKGIFWMTRADDMVVKVIRELMRRNpQVKPEMVEENVWGATTQEGDQgLTMGRTTAI 77 
                                               9********774589****************************************************** PP

                                 TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135
                                                agl+es+++++v+r+Ca g++Av+ aa +i++G++d+++aGGvE+m+++p++  a+      ++++ +
  lcl|NCBI__GCF_900129305.1:WP_073041505.1  78 LAGLSESTAGYSVDRMCAGGMTAVTCAASEIAMGACDIAIAGGVEHMGHHPMGATAD-----PNPRFLT 141
                                               ****************************************************99886.....4444444 PP

                                 TIGR01930 136 ledqllkdlvktklsmgetAenlakky.gisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.. 201
                                                +      +++++l mg+tAenl + + +i++e+ Deyal  ++ka kA++egk+++ ivp++v +k  
  lcl|NCBI__GCF_900129305.1:WP_073041505.1 142 EKL-----VSEDALVMGKTAENLHDMFpEITKEMADEYALLCQKKAFKAYQEGKIQKMIVPMTVYTKng 205
                                               333.....447789*******99988658************************************9999 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                                +v ++De++rp+ttle La+L++ f+  +g+ vt gN+s+lnDGA+ +llm+ e+akelgl+p++r+v
  lcl|NCBI__GCF_900129305.1:WP_073041505.1 206 WVVADRDEQPRPDTTLEGLASLRTPFR-VQGK-VTPGNASGLNDGACGVLLMTAEKAKELGLKPKMRLV 272
                                               8999**********************9.59*7.************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgs..ldlekvNvnGG 337
                                               ++a+agv+pe+mg+gp+p+++k+L+++gl+++d+d+vE+nEAFA+q++a+++e+g    d++++N +GG
  lcl|NCBI__GCF_900129305.1:WP_073041505.1 273 GYAFAGVKPEIMGYGPIPSTKKVLARTGLKFDDLDVVELNEAFAVQAIAFMREFGMkfPDDKRLNPYGG 341
                                               *******************************************************7543399******* PP

                                 TIGR01930 338 AiAlGHPlGasGarivltllkeLker.gkkyGlatlCvggGqGaAvile 385
                                               AiA+GHPl++sG r++++l++ ++e+ +++yGlat+Cvg+GqG +vi+e
  lcl|NCBI__GCF_900129305.1:WP_073041505.1 342 AIAFGHPLASSGPRLMVHLMHYFEEHpEARYGLATMCVGLGQGGSVIWE 390
                                               **************************999******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (398 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.48
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources